scholarly journals Comparative co-occurrence network analyses of the cichlid fish gut microbiota: community conservation and diet-associated shifts

2020 ◽  
Author(s):  
Joan Lluís Riera ◽  
Laura Baldo
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Positive Interactions ◽  
Fish Family ◽  
Comparative Analyses ◽  
Cichlid Fishes ◽  
Network Analyses ◽  
Primary Model ◽  
Microbial Associations ◽  
Microbiota Structure

AbstractCo-occurrence networks of bacteria associations are a powerful approach to explore ecologically relevant aspects of the gut microbiota structure, beyond community composition alone. Here we exploit the remarkable diversity of cichlid fishes and their multiple lake assemblages to investigate a) network features and patterns of microbial associations that were robust to major phylogeographical variables, and b) community structure changes along cichlid dietary shifts. We tackled these objectives using the large gut microbiota sequencing dataset available (nine lakes from Africa and America), building geographical and diet-specific networks and performing comparative analyses. Major findings indicated that lake and continental networks were highly resembling in global topology and node taxonomic composition, suggesting important constraints in the cichlid gut community assembling. A small fraction of the observed co-occurrence pairwises was conserved across all lake assemblages; while the origin and ecological relevance of these core associations remains unclear, their persistence suggests a potential functional role in the cichlid gut. Comparison of carnivores and herbivores-specific networks as well as mapping of diet-specific values on the African Lake Tanganyika network revealed a clear community shift as a function of diet, with an increase in complexity and node taxonomic diversity from carnivores-omnivores-plantkivores to herbivores. More importantly, diet-associated nodes in herbivores formed complex modules of positive interactions. By intersecting results from association patterns and experimental trials, future studies will be directed to test the strength of these microbial associations and predict the outcome of community alterations driven by diet.ImportanceThe gut microbiota is a complex community of interacting bacteria. Predicting patterns of co-occurrence among microbes can help understanding key ecological aspects driving community structure, maintenance and dynamics. Here we showed a powerful application of co-occurrence networks to explore gut bacteria interactions in a primary model system to study animal diversification, the cichlid fishes. Taking advantage of the large scale of phylogeographical and ecological diversity of this fish family, we built gut microbiota networks from distinct lake and continental fish assemblages and performed extensive comparative analyses to retrieve conserved and trait-specific patterns of bacteria associations. Our results identified network features that were independent from the fish biogeography and that indicated an important host selection effect on gut community assembling. Focusing on a single lake assemblage, and therefore excluding the major geographical effect, we observed that the gut microbiota structure dramatically shifted from carnivore to herbivore fishes, with a substantial increase in the number and complexity of microbial interactions.

scholarly journals Microbial co-occurrence networks of gut microbiota reveal community conservation and diet-associated shifts in cichlid fishes

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Joan Lluís Riera ◽  
Laura Baldo
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Change ◽  
Taxonomic Composition ◽  
Positive Interactions ◽  
Cichlid Fishes ◽  
Network Analyses ◽  
Microbial Network ◽  
Bacterial Associations ◽  
Experimental Trials

Abstract Background The extent to which deterministic rather than stochastic processes guide gut bacteria co-existence and ultimately their assembling into a community remains largely unknown. Co-occurrence networks of bacterial associations offer a powerful approach to begin exploring gut microbial community structure, maintenance and dynamics, beyond compositional aspects alone. Here we used an iconic model system, the cichlid fishes, with their multiple lake assemblages and extraordinary ecological diversity, to investigate a) patterns of microbial associations that were robust to major phylogeographical variables, and b) changes in microbial network structure along dietary shifts. We tackled these objectives using the large gut microbiota sequencing dataset available (nine lakes from Africa and America), building geographical and diet-specific networks and performing comparative network analyses. Results Major findings indicated that lake and continental microbial networks were highly resembling in global topology and node taxonomic composition, despite the heterogeneity of the samples. A small fraction of the observed co-occurrences among operational taxonomic units (OTUs) was conserved across all lake assemblages. These were all positive associations and involved OTUs within the genera Cetobacterium and Turicibacter and several OTUs belonging to the families of Peptostreptococcaceae and Clostridiaceae (order Clostridiales). Mapping of diet contribution on the African Lake Tanganyika network (therefore excluding the geographic variable) revealed a clear community change from carnivores (C) to omnivores (O) to herbivores (H). Node abundances and effect size for pairwise comparisons between diets supported a strong contrasting pattern between C and H. Moreover, diet-associated nodes in H formed complex modules of positive interactions among taxonomically diverse bacteria (mostly Verrucomicrobia and Proteobacteria). Conclusions Conservation of microbial network topologies and specific bacterial associations across distinct lake assemblages point to a major host-associated effect and potential deterministic processes shaping the cichlid gut microbiota. While the origin and biological relevance of these common associations remain unclear, their persistence suggests an important functional role in the cichlid gut. Among the very diverse cichlids of L. Tanganyika, diet nonetheless represents a major driver of microbial community changes. By intersecting results from predictive network inferences and experimental trials, future studies will be directed to explore the strength of these associations, predict the outcome of community alterations driven by diet and ultimately help understanding the role of gut microbiota in cichlid trophic diversification.

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

scholarly journals Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Marcus H. Y. Leung ◽  
David Wilkins ◽  
Patrick K. H. Lee
Keyword(s):  
Community Structure ◽  
Species Level ◽  
Racial Groups ◽  
Opportunistic Pathogens ◽  
Single Population ◽  
Site Specific ◽  
Skin Site ◽  
Community Membership ◽  
Network Analyses ◽  
Host Properties

Abstract Many studies have characterized microbiomes of western individuals. However, studies involving non-westerners are scarce. This study characterizes the skin microbiomes of Chinese individuals. Skin-associated genera, including Propionibacterium, Corynebacterium, Staphylococcus and Enhydrobacter were prevalent. Extensive inter-individual microbiome variations were detected, with core genera present in all individuals constituting a minority of genera detected. Species-level analyses presented dominance of potential opportunistic pathogens in respective genera. Host properties including age, gender and household were associated with variations in community structure. For all sampled sites, skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households. Network analyses highlighted general and skin-site specific relationships between genera. Comparison of microbiomes from different population groups revealed race-based clustering explained by community membership (Global R = 0.968) and structure (Global R = 0.589), contributing to enlargement of the skin pan-microbiome. This study provides the foundation for subsequent in-depth characterization and microbial interactive analyses on the skin and other parts of the human body in different racial groups and an appreciation that the human skin pan-microbiome can be much larger than that of a single population.

scholarly journals Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health

2021 ◽  
Author(s):  
Qi Yan Ang ◽  
Diana L. Alba ◽  
Vaibhav Upadhyay ◽  
Jordan E. Bisanz ◽  
Jingwei Cai ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Dietary Intake ◽  
Ethnic Groups ◽  
San Francisco ◽  
East Asian ◽  
Geographical Location ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Starting Point

Abstract Background: The human gut microbiota exhibits marked variation around the world, which has been attributed to dietary intake and other environmental factors. However, the degree to which ethnicity-associated differences in gut microbial community structure and function are maintained following immigration or in the context of metabolic disease is poorly understood.Results: We conducted a multi-omic study of 46 lean and obese East Asian and White participants living in the San Francisco Bay Area. 16S rRNA gene sequencing revealed significant differences between ethnic groups in bacterial richness and community structure. White individuals were enriched for the mucin-degrading Akkermansia muciniphila. East Asian participants had increased levels of multiple bacterial phyla, fermentative pathways detected by metagenomics, and the short-chain fatty acid end products acetate, propionate, and isobutyrate. Differences in the gut microbiota between the East Asian and White groups could not be explained by reported dietary intake, were more pronounced in lean individuals, and were associated with current geographical location. Microbiome transplantations into germ-free mice confirmed that the differences in the gut microbiota of the East Asian and White individuals we analyzed are independent of diet and that they differentially impact host body weight and adiposity in genetically identical mouse recipients.Conclusions: The reported findings emphasize the utility of studying diverse ethnic groups within a defined geographical location and provide a starting point for dissecting the mechanisms contributing to the complex interactions between the gut microbiome and ethnicity-associated lifestyle, demographic, metabolic, and genetic factors.

scholarly journals Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation

mSystems ◽  
2021 ◽  
Author(s):  
Evgenii I. Olekhnovich ◽  
Artem B. Ivanov ◽  
Vladimir I. Ulyantsev ◽  
Elena N. Ilina
Keyword(s):  
Gut Microbiota ◽  
Antibiotic Resistance Genes ◽  
Host Immunity ◽  
Third Party ◽  
Colonization Resistance ◽  
Fecal Transplantation ◽  
Antimicrobial Substances ◽  
Functional Features ◽  
Microbiota Structure

We assumed that the enrichment of successful gut microbes by lantibiotic/antibiotic resistance genes can be related to gut microbiota colonization resistance by third-party microbe phenomena and resistance to bacterium-derived or host-derived antimicrobial substances. According to this assumption, competition between the donor-derived and recipient-derived microbes as well as host immunity may play a key role in the FMT-related colonization and redistribution of recipient gut microbiota structure.

scholarly journals High Throughput Analysis Reveals Changes in Gut Microbiota and Specific Fecal Metabolomic Signature in Hematopoietic Stem Cell Transplant Patients

2021 ◽  
Vol 9 (9) ◽  
pp. 1845
Author(s):  
Soumaya Kouidhi ◽  
Nessrine Souai ◽  
Oumaima Zidi ◽  
Amor Mosbah ◽  
Amel Lakhal ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gut Microbiota ◽  
Hematopoietic Stem Cell ◽  
Metabolic Pathways ◽  
Gas Chromatography Mass Spectrometry ◽  
Resistant Bacteria ◽  
Positive Interactions ◽  
Cell Transplant ◽  
Hematopoietic Stem ◽  
Transplant Patients

There is mounting evidence for the emerging role of gut microbiota (GM) and its metabolites in profoundly impacting allogenic hematopoietic stem cell transplantation (allo-HSCT) and its subsequent complications, mainly infections and graft versus host-disease (GvHD). The present study was performed in order to investigate changes in GM composition and fecal metabolic signature between transplant patients (n = 15) and healthy controls (n = 18). The intestinal microbiota was characterized by NGS and gas chromatography–mass spectrometry was employed to perform untargeted analysis of fecal metabolites. We found lower relative abundances of Actinobacteria, Firmicutes, and Bacteroidetes and a higher abundance of Proteobacteria phylum after allo-HSCT. Particularly, the GvHD microbiota was characterized by a lower relative abundance of the short-chain fatty acid-producing bacteria, namely, the Feacalibacterium, Akkermansia, and Veillonella genera and the Lachnospiraceae family, and an enrichment in multidrug-resistant bacteria belonging to Escherichia, Shigella, and Bacteroides. Moreover, network analysis showed that GvHD was linked to a higher number of positive interactions of Blautia and a significant mutual-exclusion rate of Citrobacter. The fecal metabolome was dominated by lipids in the transplant group when compared with the healthy individuals (p < 0.05). Overall, 76 metabolites were significantly altered within transplant recipients, of which 24 were selected as potential biomarkers. Furthermore, the most notable altered metabolic pathways included the TCA cycle; butanoate, propanoate, and pyruvate metabolisms; steroid biosynthesis; and glycolysis/gluconeogenesis. Specific biomarkers and altered metabolic pathways were correlated to GvHD onset. Our results showed significant shifts in gut microbiota structure and fecal metabolites characterizing allo-HSCT.

scholarly journals The Association between Gut Microbiota and Uremia of Chronic Kidney Disease

2020 ◽  
Vol 8 (6) ◽  
pp. 907 ◽  
Author(s):  
Ji Eun Kim ◽  
Hyo-Eun Kim ◽  
Ji In Park ◽  
Hyunjeong Cho ◽  
Min-Jung Kwak ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Gut Microbiota ◽  
Kidney Function ◽  
Kidney Diseases ◽  
Toxin Production ◽  
Positive Interactions ◽  
Uremic Toxin ◽  
Serum Concentrations ◽  
Pyruvate Metabolism

Chronic kidney disease (CKD)-associated uremia aggravates—and is aggravated by—gut dysbiosis. However, the correlation between CKD severity and gut microbiota and/or their uremic metabolites is unclear. We enrolled 103 CKD patients with stage 1 to 5 and 46 healthy controls. We analyzed patients’ gut microbiota by MiSeq system and measured the serum concentrations of four uremic metabolites (p-cresyl sulfate, indoxyl sulfate, p-cresyl glucuronide, and trimethylamine N-oxide) by liquid chromatography–tandem mass spectrometry. Serum concentrations of the uremic metabolites increased with kidney function deterioration. Gut microbial diversity did not differ among the examined patient and control groups. In moderate or higher stage CKD groups, Oscillibacter showed positive interactions with other microbiota, and the proportions of Oscillibacter were positively correlated with those of the uremic metabolites. The gut microbiota, particularly Oscillibacter, was predicted to contribute to pyruvate metabolism which increased with CKD progression. Relative abundance of Oscillibacter was significantly associated with both serum uremic metabolite levels and kidney function. Predicted functional analysis suggested that kidney-function-associated changes in the contribution of Oscillibacter to pyruvate metabolism in CKD may greatly affect the gut environment according to kidney function, resulting in dysbiosis concomitant with uremic toxin production. The gut microbiota could be associated with uremia progression in CKD. These results may provide basis for further metagenomics analysis of kidney diseases.

scholarly journals Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Debra Poutsiaka ◽  
Lori Stern ◽  
Virginia Riquelme ◽  
Emily Hollister ◽  
Julia Cope ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Lactobacillus Rhamnosus ◽  
Detailed Examination ◽  
Global Changes ◽  
Shotgun Metagenomics ◽  
Gene Abundance ◽  
Funding Sources ◽  
And Function ◽  
Relative Gene

Abstract Objectives This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI. Methods Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group). Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes. Results Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25. Conclusions We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI. Funding Sources Pfizer Inc.

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